def _create_variants_report(self):
"""
Creates and returns a variants report.
"""
from pbreports.report.variants import make_variants_report
from test_pbreports_report_variants import VARIANTS_DATA as datadir
log.info(
'Creating variants report using datadir {d}'.format(d=datadir))
als = os.path.join(datadir, 'alignment_summary.gff')
variants = os.path.join(datadir, 'variants.gff.gz')
ref = os.path.join(datadir, 'ecoliK12_pbi_March2013')
make_variants_report(als, variants, ref, 25,
'variants.json', self._output_dir, 60, False)
return self._deserialize_report(os.path.join(self._output_dir, 'variants.json'))
def _create_variants_report(self):
"""
Creates and returns a variants report.
"""
from pbreports.report.variants import make_variants_report
from test_pbreports_report_variants import VARIANTS_DATA as datadir
log.info(
'Creating variants report using datadir {d}'.format(d=datadir))
als = os.path.join(datadir, 'alignment_summary.gff')
variants = os.path.join(datadir, 'variants.gff.gz')
ref = os.path.join(datadir, 'ecoliK12_pbi_March2013')
make_variants_report(als, variants, ref, 25, 'variants.json',
self._output_dir, 60, False)
return self._deserialize_report(
os.path.join(self._output_dir, 'variants.json'))
def test_make_variants_report(self):
"""
Create a report object, do assertions on its properties, then assert that it gets written
"""
report = make_variants_report(self.ALIGNMENT_SUMMARY, self.VARIANTS_GFF, self.REFERENCE, 25, 'rpt.json', self._output_dir, 60, False)
self.assertEqual(5, len(report.attributes))
self.assertEqual(1, len(report.tables))
self.assertEqual(1, len(report.plotGroups))
self.assertIsNotNone(report.plotGroups[0].legend)
self.assertTrue(op.exists(op.join(self._output_dir, 'rpt.json')))
def test_make_variants_report(self):
"""
Create a report object, do assertions on its properties, then assert that it gets written
"""
report = make_variants_report(self.ALIGNMENT_SUMMARY,
self.VARIANTS_GFF, self.REFERENCE, 25,
'rpt.json', self._output_dir, 60, False)
self.assertEqual(5, len(report.attributes))
self.assertEqual(1, len(report.tables))
self.assertEqual(1, len(report.plotGroups))
self.assertIsNotNone(report.plotGroups[0].legend)
self.assertTrue(op.exists(op.join(self._output_dir, 'rpt.json')))
def test_make_variants_report_invalid_input_files(self):
"""
inputs cannot be null or non-existent
"""
# als tests
with self.assertRaises(PbReportError):
make_variants_report(None, self.VARIANTS_GFF, self.REFERENCE, 'foo.json', 1, self._output_dir, '1', False)
with self.assertRaises(IOError):
make_variants_report('foo', self.VARIANTS_GFF, self.REFERENCE, 'foo.json', 1, self._output_dir, '1', False)
# variants tests
with self.assertRaises(PbReportError):
make_variants_report(self.ALIGNMENT_SUMMARY, None, self.REFERENCE, 'foo.json', 1, self._output_dir, '1', False)
with self.assertRaises(IOError):
make_variants_report(self.ALIGNMENT_SUMMARY, 'foo', self.REFERENCE, 'foo.json', 1, self._output_dir, '1', False)
# ref tests
with self.assertRaises(PbReportError):
make_variants_report(self.ALIGNMENT_SUMMARY, self.VARIANTS_GFF, None, 'foo.json', 1, self._output_dir, '1', False)
with self.assertRaises(IOError):
make_variants_report(self.ALIGNMENT_SUMMARY, self.VARIANTS_GFF, 'foo', 'foo.json', 1, self._output_dir, '1', False)
def test_make_variants_report_invalid_input_files(self):
"""
inputs cannot be null or non-existent
"""
# als tests
with self.assertRaises(PbReportError):
make_variants_report(None, self.VARIANTS_GFF, self.REFERENCE,
'foo.json', 1, self._output_dir, '1', False)
with self.assertRaises(IOError):
make_variants_report('foo', self.VARIANTS_GFF, self.REFERENCE,
'foo.json', 1, self._output_dir, '1', False)
# variants tests
with self.assertRaises(PbReportError):
make_variants_report(self.ALIGNMENT_SUMMARY, None, self.REFERENCE,
'foo.json', 1, self._output_dir, '1', False)
with self.assertRaises(IOError):
make_variants_report(self.ALIGNMENT_SUMMARY, 'foo', self.REFERENCE,
'foo.json', 1, self._output_dir, '1', False)
# ref tests
with self.assertRaises(PbReportError):
make_variants_report(self.ALIGNMENT_SUMMARY, self.VARIANTS_GFF,
None, 'foo.json', 1, self._output_dir, '1',
False)
with self.assertRaises(IOError):
make_variants_report(self.ALIGNMENT_SUMMARY, self.VARIANTS_GFF,
'foo', 'foo.json', 1, self._output_dir, '1',
False)
def run_report(args):
return make_variants_report(args.aln_summ_gff, args.variants_gff, args.reference, args.maxContigs,
args.report, args.output, args.dpi, args.dumpdata)
